Certain medical devices such as tissue removal catheters require cleaning to remove collected debris. For example, some tissue removal catheters include a tissue collection chamber that collects excised tissue and other debris that is cut away or otherwise extracted from a vascular or other biological lumen. When tissue collection chambers become full they can be cleaned to empty the collected tissue. Certain cleaning tools have been developed to aid in cleaning the tissue collection chambers of tissue removal catheters. In one example, a cleaning tool is received on the distal tip of an atherectomy catheter until it visually appears that the device is in an operative position. A proximal Touhy Borst seal of the cleaning tool is manually actuated to seal a flushing lumen of the cleaning device about the catheter, and flushing fluid is imparted into the flushing lumen.